diff goseq.xml @ 9:ef2ad746b589 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit e230a8db9e090c6e0ea9577863ec6153df79e145"

--- a/goseq.xml	Fri Sep 06 07:50:46 2019 -0400
+++ b/goseq.xml	Sun Jun 06 22:47:36 2021 +0000
@@ -1,18 +1,27 @@
 <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@">
     <description>tests for overrepresented gene categories</description>
+    <xrefs>
+        <xref type="bio.tools">goseq</xref>
+    </xrefs>
+    <edam_topics>
+        <edam_topic>topic_3308</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2436</edam_operation>
+    </edam_operations>
     <macros>
-        <token name="@VERSION@">1.36.0</token>
+        <token name="@VERSION@">1.44.0</token>
         <token name="@GALAXY_VERSION@">galaxy0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement>
-        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
-        <requirement type="package" version="0.8.3">r-dplyr</requirement>
-        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
-        <requirement type="package" version="1.6.2">r-optparse</requirement>
+        <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement>
+        <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement>
+        <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="1.0.6">r-dplyr</requirement>
+        <requirement type="package" version="3.3.3">r-ggplot2</requirement>
+        <requirement type="package" version="1.6.6">r-optparse</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -194,7 +203,7 @@
             <output name="top_plot" ftype="pdf" file="topgo.pdf" compare="sim_size"/>
             <output name="wallenius_tab">
                 <assert_contents>
-                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
+                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
                     <has_text_matching expression="GO:0000278.*0.01" />
                 </assert_contents>
             </output>
@@ -226,13 +235,13 @@
             </section>
             <output name="wallenius_tab">
                 <assert_contents>
-                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
-                    <has_text_matching expression="GO:0005576.*9.0" />
+                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
+                    <has_text_matching expression="GO:0005576.*0.9" />
                 </assert_contents>
             </output>
             <output name="cat_genes_tab">
                 <assert_contents>
-                    <has_text_matching expression="Categories.*DEgenes" />
+                    <has_text_matching expression="category.*de_genes" />
                     <has_text_matching expression="GO:0005615.*ENSG00000090402,ENSG00000108953,ENSG00000070961" />
                 </assert_contents>
             </output>
@@ -264,8 +273,8 @@
             </section>
             <output name="wallenius_tab">
                 <assert_contents>
-                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" />
-                    <has_text_matching expression="GO:0016569.*0.8" />
+                    <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p_adjust_over_represented.*p_adjust_under_represented" />
+                    <has_text_matching expression="GO:0016569.*0.90" />
                 </assert_contents>
             </output>
         </test>
@@ -438,7 +447,7 @@
 Example:
 
 =========== =============== ================ ============ ========== ======================================== ========== =================== ====================
-*category*  *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term*                                   *ontology* *p.adjust.over_rep* *p.adjust.under_rep*
+*category*  *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term*                                   *ontology* *p_adjust_over_rep* *p_adjust_under_rep*
 ----------- --------------- ---------------- ------------ ---------- ---------------------------------------- ---------- ------------------- --------------------
 GO\:0005576  0.000054        0.999975         56           142       extracellular region                     CC         0.394825             1
 GO\:0005840  0.000143        0.999988         9            12        ribosome                                 CC         0.394825             1